Valine-restricted diet regulates DNA methylation [ddC S1-END-Seq]

The abundancy of intracellular amino acid (AA) levels is precisely sensed by complex machineries to regulate various signaling pathways and control cell functions. Insufficient intracellular AAs may block the release of tRNA molecules from the general control non-derepressible 2 (GCN2), and consequently activate GCN2-ATF4 pathways, which is an indirect mechanism for sensing general AAs levels. Additionally, the intracellular levels of some AAs can be sensed by direct binding to specific sensors. Nowadays, the sensors of arginine and leucine levels are most well-characterized, including CASTor1/2, SLC38A9, Sestrin2 and SAR1B, which regulate the mechanistic target of rapamycin complex 1 (mTORC1) pathway, and couple AA availability to cell growth and metabolism. However, it is still unclear whether and how other types of amino acids are directly sensed to regulate cellular functions except tRNA synthetases. Moreover, epigenetics is known to be regulated by the metabolism of amino acids, but it is incompletely understood how AA abundancy regulates the epigenetics, especially DNA methylation. The long-sought sensor of amino acids for epigenetic regulation has thus far been unknown. Here, we present evidence that valine sensor regulated DNA demethylation. Overall design: ddC S1-END-seq in WT and TDG knockdown HCT116 cells upon valine deprivation

细胞内氨基酸（AA）的丰度可通过复杂的蛋白复合物精准感知，以此调控多条信号通路并控制细胞功能。细胞内氨基酸匮乏会阻断转运RNA（tRNA）从通用控制非阻遏蛋白2（GCN2）的释放，进而激活GCN2-ATF4信号通路，这是感知整体氨基酸水平的间接调控机制。此外，部分氨基酸的细胞内水平可通过与特定感受器直接结合的方式被感知。
目前，研究最为透彻的氨基酸感受器为精氨酸与亮氨酸感受器，包括CASTor1/2、SLC38A9、Sestrin2及SAR1B，它们可调控雷帕霉素靶蛋白复合物1（mTORC1）信号通路，并将氨基酸的可获得性与细胞生长及代谢过程相耦联。然而，除氨酰-tRNA合成酶外，其他类型氨基酸是否可通过直接感知的方式调控细胞功能，以及其具体调控机制仍不明确。
此外，已知氨基酸代谢可调控表观遗传学，但氨基酸丰度如何调控表观遗传学过程（尤其是DNA甲基化）的机制仍未完全阐明。长期以来人们一直探寻的、参与表观遗传调控的氨基酸感受器迄今仍未被发现。本研究提供证据表明，缬氨酸感受器可调控DNA去甲基化过程。
整体实验设计：在缬氨酸剥夺处理的野生型（WT）及胸腺嘧啶DNA糖苷酶（TDG）敲低HCT116细胞中开展ddC S1-END-seq实验。